Focusing on European population genetics and modern physical anthropology.

search this blog

Thursday, March 2, 2017

Baltic Corded Ware: rich in R1a-Z645

An important preprint has just appeared at bioRxiv. It includes ancient DNA from four Estonian Corded Ware Culture (CWC) individuals from two different sites.
These CWC samples belong to Y-haplogroup R1a-Z645, which is the most common type of R1a in the world today, including South Asia, despite a relatively recent coalescent time of 5,400 yr BP. One of the samples is further classified as belonging to R1a-Z283. Almost 100% of the modern-day Eastern and Central European R1a belongs to this subclade.

The new data also includes an Comb Ceramic Culture (CCC) male that belongs to R1a5-­YP1272. This might be an extinct line, or one that is now extremely rare in Eastern Europe. From the paper:

All four of the Estonian CWC individuals could be assigned to the R1a-Z645 sub-clade of hg R1a-M417 which together with N is one of the most common Y chromosome haplogroups in present-day Estonians (33%) [44] . Importantly, this R1a lineage is only distantly related to the R1a5 lineage we found in the CCC sample. The finding of high frequency of R1a-M417 in Estonian CWC samples is consistent with the observations made for other Corded Ware sites that, along with Late Bronze Age remains associated with Sintashta Culture, also show high frequency of hg R1a-M417 [2,25].
...
The coalescent time for the R1a-Z645 clade, estimated from modern data at 5,400 yr BP (95% CI 4,950–6,000) 43 , predates the time when the CWC individuals carrying the R1a-Z645 lineages lived in Estonia (4,000–4,800 yr BP). The fact that all four of the CWC male individuals from two distinct sites in Estonia belonged to this recently expanded R1a branch, different from the one carried by CCC, suggests that admixture between CWC farmers and CCC hunter-gatherers may have been limited at least in the male lineages during the early stages of farming in Estonia.

Now, can anyone explain to me how the authors came to this conclusion? Was it based on their ADMIXTURE output?

Furthermore, the presence of a genetic component associated with Caucasus hunter-gatherers and later with people representing the Yamnaya Culture in Eastern hunter-gatherers and Estonian CCC individuals means that the expansion of the CWC cannot be seen as the sole means for the spread of this genetic component, at least in Eastern Europe.

If it is indeed based on ADMIXTURE, then they really need to back it up with some robust formal stats and qpAdm, because ADMIXTURE is not a formal mixture test.
Moreover, they used the projection (P) option in their ADMIXTURE analysis. I'm not a huge fan of this option when running fine scale intra-continental analyses, because I find that it usually results in severe projection bias. In other words, the test samples are treated differently from the reference samples, and essentially show results that they shouldn't.
Speaking of projection bias, I'm quite certain that their Principal Component Analysis (PCA) suffers from it. The ancient samples look like they're being pulled into the middle of the plot, so much so that one of the foragers basically clusters with modern-day Lithuanians, while the CWC individuals appear too western. They need to fix this.

I do note that the authors used the lsqproject option when running their PCA. A lot of people assume that once they do this they've taken care of projection bias. This is not so. lsqproject doesn't solve this problem; it just makes sure that missing markers don't skew the projection.
Citation...
Saag et al., Extensive farming in Estonia started through a sex-biased migration from the Steppe, bioRxiv, March 2, 2017, doi: https://doi.org/10.1101/112714

Oh another IRRELEVANT SAMPLE? geez seems like the majority of samples are irrelevant nowadays, what are the odds!?

Furthermore, the presence of a291 genetic component associated with Caucasus hunter-gatherers and later with people292 representing the Yamnaya Culture in Eastern hunter-gatherers and Estonian CCC individuals293 means that the expansion of the CWC cannot be seen as the sole means for the spread of this294 genetic component, at least in Eastern Europe. The transition to intensive farming and animal295 husbandry in Estonia, which took place a few thousand years after the farming transition in296 many other parts of Europe, was conveyed by the CWC individuals and involved an influx of297 new genetic material. These people carried a clear Steppe ancestry with some minor Anatolian298 contribution, most likely absorbed through female lineages during the population movements.

I don't disagree that the majority of European R1a is from Corded Ware, but R1a was all over the Corded Ware horizon prior to the existence of Corded Ware obviously, going back to the Mesolithic so it's a rather redundant statement. It certainly isn't from Yamnaya, and we can say certainly now that Eastern CWC isn't Yamnaya derived.

I don't disagree that the majority of European R1a is from Corded Ware, but R1a was all over the Corded Ware horizon prior to the existence of Corded Ware obviously, going back to the Mesolithic so it's a rather redundant statement. It certainly isn't from Yamnaya, and we can say certainly now that Eastern CWC isn't Yamnaya derived.

But Corded War is from the steppe, because early Corded Ware resemble Yamnaya.

So how do you know that R1a-Z645 isn't from the steppe or even from western Yamnaya? We already know that there was R1a on the steppe.

Does anyone know what this statement in the paper is based on? Are they referring to their ADMIXTURE analysis here or what?

Furthermore, the presence of a genetic component associated with Caucasus hunter-gatherers and later with people representing the Yamnaya Culture in Eastern hunter-gatherers and Estonian CCC individuals means that the expansion of the CWC cannot be seen as the sole means for the spread of this genetic component, at least in Eastern Europe.

If this is based on ADMIXTURE output, rather than formal stats and models, then it's bullshit.

DaveOne cannot castigate people for still seeing the possibility that not every single expanding lineage moved out from the steppe. R1a , R1b, I2 all existed over a broad area of C - E Europe, and thus -** at least in theory**- there was a "kurganization" of a chain of cultures through cultural borrowing and exogamy. Even the peer reviewed papers suggest this. Although not a formal test, I already demonstrated this with nMonte.

@DavidskiWhat I wrote is correct. Basically 100% of Eastern European R1a is from Corded Ware. That means a massive amount of Eastern European ancestry is from Corded Ware.

Ha-ha-ha. Basically 100% of modern Eastern European R1a is from Maykop -> Catacomb cultures. Those R1a-Z645 CWC folks at the first place came in steppe from Maykop culture (influx of Maykop pops in western Yamnaya) and only then they migrated in Estonia.

Good , god , pardon me if I wrote wrong . I am saying, that do you consider, to the possibility, that these early R1a expansions , can explain the suggested IE type substratum influence seen in Uralic languages?, as suggested by some.

Good, god, pardon me if I wrote wrong. I am saying, that do you consider, to the possibility, that these early R1a expansions, can explain the suggested IE type substratum influence seen in Uralic languages?, as suggested by some.

I suppose yes, if there were twin expansions from the steppe to the Baltic and the forest steppe by Z645 populations, as the presence of Z645 Poltavka outlier at ~4,500 BP Samara suggests.

Beautiful study from a very skilled and cautious labs!! Clearly R1a-Z645 is the marker of CWC while earlier versions of R1a were "pandemic" across Eastern Europe during the Mesolithic/CCC Eras. The expansion time of R1a-Z645 from YFull (as I mentioned in an earlier posting) is 5000 ybp which fits with the Estonian radiocarbon dating for CWC is Estonia. Parsimony dictates that R1a-Z645 likely expanded rapidly from "somewhere" Steppes/North Caucasus etc... and influenced the transition from CCC to CWC. IMO. it is inconceivable that Z645 originated further south and expanded so readily in Europe. I'm very familiar with the PC analysis from this group having collaborated frequently with them in modern DNA studies, so I don't find the PC plot particularly troublesome. CWC was a hybrid culture and rapidly spread incorporating many other local cultures where they settled and was male-mediated in large part.

I think it is Admixture that they're misinterpreting. They're probably referring to the CHG that shows up in EHG, along with Siberian, to compensate for no EHG component. They may be mistaking that for real Caucasus ancestry.

@Davidski,Being more of a numbers/algebraic guy with impoverished visual-spatial skills, I'll defer to your perceptions! But looking at the forest rather than the trees, the PC plot makes broad sense to me. I am very aware how sampling can influence the look of a PC plot!

"CWC was a hybrid culture and rapidly spread incorporating many other local cultures where they settled and was male-mediated in large part."

Whilst no doubt bands of men were involved, we need to recall the discussion between Kristiina & I that male haploid lineages always have lower Ne. Secondly, the Y DNA landscape of CWC is not 100% homogeneous. There is R1b in central Poland CWC, R1a x Z645 in Germany, possibly some non-R1a (? I, ?G) in an older Polish CWC study, and R1a –Z645 in this east Baltic study.

Yes, of course, the model is simplistic and needs to be nuanced. What I'm arguing is that, as an outsider to the steppe hypothesis with absolutely no "confirmation bias", (I am a socialist pacifist post-colonial/feminist scholar) the steppe hypothesis that Davidski has presented holds scientific traction.

Roy king,Perhaps its nothing, but green component is everywhere!, also in Mal'ta... and the greenest is Iran and modern Kalash , I mean in the admixture itself .It seems that every R1a has green component .Also EHG and Iran N is more or less the same amount as CHG .what is funny is that Ust-Ishim is a patchwork of components . Also Mal'ta in not bad. So this ANE component seems rather a big mix . Pardon if its totally wrong .

@ RoyHa ha; bless you.But my point was that a statement like "Clearly R1a-Z645 is the marker of CWC " is demonstrably wrong. I donl;t think anyone doubts a steppe connection. That's been recognised since the days of Carlton Coon. The real question is the real nature of interaction, and whjether the "Yamnaya big bang" theory is actually correct, or a simplistic abstraction.

The Ne of the Y chromosome in this period is unusually low compared to that for mtDNA, however, in a ratio of approx 1:50 for Europe, as opposed to a usual ration ~1:3 or 1:4. So the social dynamics here are not simply about the usual variance in male reproductive success being higher than the female variance, which characterises all societies in general and causes the lower, but still skewed, ratio, in most time periods. The period of IE movement was characterised by unusual social mechanisms that influenced the Y chromosome only, leaving the Ne of mtDNA untouched. Since these were simple societies though, nothing like the extreme Arab-sheikh style polygamy could have occurred, since that requires a level of stable social stratification that the CW and Yamnaya most certainly did not possess.

So Corded Ware and not just M417 are now from Maykop? I'm glad you move with the data.

Go and redraw your maps.

There's no need to redraw my maps. They are OK. Sredny Stog(first wave of migrants from the Iranian Plateau) was predominantly R1a-YP1272. Maykop (second wave of R1a migrants) was predominantly R1a-M417/Z645. Influx of R1a-Z645 folks from Maykop in Sredny Stog resulted in cultural transition of Sredny Stog into w.Yamnaya (decrease of R1a-YP1272 and rise of R1a-M417/Z645). And finally population of Maykop culture expanded in the PC steppe and banished w.Yamnaya folks (R1a-YP1272 and R1a-M417/Z645). Obviously there were more R1a-M417/Z645 folks in CWC than I initially thought but anyway major subclades below R1a-M417/Z645 came from Maykop->Catacomb culture.

Rob, estimates for Ne are just that--estimates from coalescent simulations and equations. They are only 'overestimates' if we attempt to 'fit' them with our usual intuitions about polygamy in a panmictic society, which implies that the rates of polygamy must have been extremely high over multiple generations, well outside the rates we see empirically in small-scale societies today. There must be some other social mechanism that accounts for both the intensity of the bottleneck during the invasion and its rapid recovery during the Iron Age.

Blundering in, the general PCA plot looks exactly like the plot used in Lazaridis 2016 with the addition of these 7 new samples - http://i.imgur.com/SvpMahB.png.

If all the ancients are projected, I would think that they would all be compressed towards the middle, but none particularly more so than others. So Kud2 and Kud3 should still have the same relative position more or less to EHG, CHG, WHG, etc, and its their position relative to modern samples that may be underestimated?

J1c took up a large fraction of EEF's mtDNA. It's one of the defining mHGs of EEF. Today both T2a1a and J1c3 can be called European haplogroups.

U5b1d1 is very rare today. Denmark and Italy are the only locations where it has been found as far as I know. I don't know much about U5b1b though. It's popular in Finnish, Saami, and Karelians in the form of two founder effects; U5b1b2 and U5b1b1a.

In the admixture run, Estonian CWC does not have much farmer ancestry (orange, EEF+Anatolia Neolithic). Kunila2 has more farmer ancestry (c. 7%) than most others and it has almost as much ENA as farmer ancestry.

Kunila2's mtdna is J1c3, and it is a typical EEF lineage. Also Sope (both Sope_d and Sope_r?) is more farmer than most others and its mtDNA is H5a. H5 has been detected in Neolithic Lengyel Brześć Kujawski Poland, in Neolithic Rossen Wittmar Germany, and Middle Neolithic Blätterhöhle Germany and Regional TRB Bernburg Benzingerode.

Ardu1 and 1r are T2a1, and it is a typical Yamnaya lineage (detected e.g. in Dnieper Yamnaya Vinogradnoe Ukraine).

U5b2c is not Yamnaya but a local forager line and detected at least in HohlensteinStadel Germany 8,6 kya. U5b1b is also a local forager line and detected in Kunda and Narva samples.

On the basis of mtDNA, there are three sources: local foragers, (Polish) Neolithic farmers and Dnieper Yamnaya.

@Kristiina“On the basis of mtDNA, there are three sources: local foragers, (Polish) Neolithic farmers and Dnieper Yamnaya.”By (Polish) Neolithic farmers you mean CWC, because there were no other Neolithic farmer migrations from Poland to Estonia at that time.

H5a1 with mutation 15833 is quite young and was estimated to date around 4000 BP which roughly corresponds to Estonian CWC Sope sample 4,575–4,350 BP.

“Recent studies on mtDNA hg H5 have revealed that phylogenetically older subbranches, H5a3, H5a4 and H5e, are observed primarily in modern populations from southern Europe, while the younger ones, including H5a1 that was found among RoIA individuals in our study, date to around 4.000 years ago (kya) and are found predominantly among Slavic populations of Central and East Europe, including contemporary Poles”.

So H5a1 with mutation 15833 was probably a wife of CWC man with R1a-Z645/Z283. Her sisters stayed in Poland and it is now a Slavic marker.It is important for determining what language CWC spoke. Was it Indo-Slavic, Balto-Slavic or some early Slavic.

I guess that for some reason the Iberian samples act as a good proxy for whatever group these guys got their "wives" from. It seems to be related to the Levant too, so maybe this is related to some admixture that already took place in the North Caucasus itself and shows up as Iberian (mix of Euro_MN with some Levant?).

"What does it mean? Steppe men were importing Iberian wives for their move north ?"

It doesn't mean anything other than that the X chromosomes of the Neolithic farmers were very homogeneous (similar to Levant Neolithic and Anatolia Chalcolithic), and that the CWC and the Neolithic/Early Bronze Age Iberians also had the most of these chromosomal component. Meaning that thise populations had the highest ratio of female Neolithic X vs anything else X.

Y chromosomesWe determined the sex of the eight individuals by examining the ratio of reads aligning to the X and Y chromosomes44. We determined the Y-chromosome haplogroup of four male individuals using the nomenclature of the International Society of Genetic Genealogy (www.isogg.org).Individual I0563 (Pazyryk) belonged to the Z93 clade45 which is frequent in Central Asia45,46 and was also recorded in Bronze Age individuals from Mongolia47 and the Sintashta culture from Samara33. Individual I0577 (Aldy Bel) also belonged to haplogroup R1a1a1b but could not be determined more downstream. Individual I0575 (Sarmatian) belonged to haplogroup R1b1a2a2, and was thus related to the dominant Ychromosome lineage of the Yamnaya (Pit Grave) males from Samara37 (~3000BCE).Individual IS2 belonged to haplogroup Q1a which was also found in the Eneolithic period in Samara33 in Europe but is most commonly found in present-day people from Siberia and the Americas48 (Supplementary Table 22).

What does it mean? Steppe men were importing Iberian wives for their move north ?

or

I guess that for some reason the Iberian samples act as a good proxy for whatever group these guys got their "wives" from. It seems to be related to the Levant too, so maybe this is related to some admixture that already took place in the North Caucasus itself and shows up as Iberian (mix of Euro_MN with some Levant?).

@Alberto,why would a Mix taking place in North Caucasus looks like Iberian? - lol

Just to summarise:1)We need to see the results of Maykop and Western Yamnaya from the territory of Ukraine to close the case with Indo-European origins for good. 2)The paper on Bell beakers would be really informative to outline the history of modern R1b-M269 in Central and Western Europe. I suspect CWC had nothing to do with the spread of R1b in Europe. Its aDNA results prove to be predominantly R1a. My bet would be on Balkan-Pannonian Urheimat for Bell Beakers that hosted one of the forward Steppe groups. Thus amalgamation of Yamnaya and Vucedol culture can best explain the common Dinaric anthropological type of Bell Beakers.

If R1a-Z645 and Z283 are both found in CWC, and CWC is a strong candidate for speaking IE, I don't see why the trolls are still out in full force refuting this claim. If Z93 descends from Z645, and based on this data, certainly further supports the eastern branches of IE spreading from the west with R1a-Z645(xZ283) males. Not sure how the trolls can argue against this point.

1 At the two LCT loci associated with lactase persistence, the derived allele is observed only in heterozygotes, only in the eastern Scythian samples, and at low frequency (2–3%).

2 mtDNA on p. 29, Y Hgs on p.55 and p.71

3 The most interesting part for me was that Eastern Scythians have made their mark on Turkic populations more than others,

For western Scythian-era samples, contemporary populations with high statistical support for a genealogical link are located mainly in close geographical proximity, whereas contemporary groups with high statistical support for descent from eastern Scythians are distributed over a wider geographical range. Contemporary populations linked to western Iron Age steppe people can be found among diverse ethnic groups in the Caucasus, Russia and Central Asia (spread across many Iranian and other Indo-European speaking groups), whereas populations with genetic similarities to eastern Scythian groups are found almost exclusively among Turkic language speakers (Supplementary Figs 10 and 11).

Contemporary descendants of western Scythian groups are found among various groups in the Caucasus and Central Asia, while similarities to eastern Scythian are found to be more widespread, but almost exclusively among Turkic language speaking (formerly) nomadic groups, particularly from the Kipchak branch of Turkic languages (Supplementary Note 1). The genealogical link between eastern Scythians and Turkic language speakers requires further investigation, particularly as the expansion of Turkic languages was thought to be much more recent—that is, sixth century CE onwards—and to have occurred through an elite expansion process. There are potentially many more demographic factors involved in the origins of Turkic language speakers, such as migration waves associated with Xiongnu, ancient Turkic or early Mongolian populations. The extent to which the eastern Scythians were involved in the early formation of Turkic speaking populations can be elucidated by future genomic studies on the historic periods following the Scythian times.

4 Scythians and Sarmatians were supposed to have spoken Iranian languages. The paper suggests a model of multiregional origins for Scythian samples rather than a purely Western Eurasian steppe origin, though the paper also mentions there was notable genetic connection between the two.

Did the Eastern Scythians adopt Turkic? Or did many eastern kinds never speak Iranian but some pre-proto-Turkic despite cultural and some genetic links? Or does the genetic and cultural connection between the eastern and western IA steppe samples imply that the Eastern Scythians evolved Turkic from Iranian?

And can Turkic ethnogenesis be described as Indo-European by genetics (ancestry) but not by language?

"while the younger ones, including H5a1 that was found among RoIA individuals in our study, date to around 4.000 years ago (kya) and are found predominantly among Slavic populations of Central and East Europe, including contemporary Poles”."

So, that sample is Iron Age Przeworsk Gąski. Brześć Kujawski H5 is from 4500 BC.

"And can Turkic ethnogenesis be described as Indo-European by genetics (ancestry) but not by language?"

Turkic languages have a quite modern expansion. The Turkic speaking peoples clearly have Scythian ancestry, which is not surprising. But, overall, they have a highly mixed ancestry from highly mobile and/or very successful groups. It is amazing that Turkish languages are so widespread, but the same goes for Indo-European. The geography of Central Asia is easy to cross with the right vehicles.

Interesting figures in the paper's SI on pages 13 to 17, for which page 50 has the abbreviations. Particularly p.17's Supplementary Figure 11.

There is some distinction visible here between Brahui and Baloch in terms of their varying descent and ancestral relatedness to Eastern and Western Scythians.

The Caucasus, parts of Iran and Brahui, Baloch and Pathans are designated as having high ancestral relatedness (green and black) to both the Eastern and Western Scythians.

Kalash however are depicted as high in descent from the Western Scythian samples in comparison to many of their immediate neighbours to the south, excepting the Hazara who are thought to have some Turkic or Mongolian ancestry from more recent central Asian migrations. Does this imply the Kalash are a significantly Western Scythian population?

Although several Caucasus populations were compared, I would have liked it if the paper had also compared the Ossetians against the Sarmatian samples at least, since Ossetians are supposed to be direct descendants of some Sarmatian tribes.

It doesn't seem like Eurasian populations further northwest than the Caucasus and Russia were considered. I'm interested to know if modern Hungarians have a high relation to Scythians and Sarmatians too, as a connection to one or both has frequently been suggested. Comparisons with Baltic and more western populations like Germanic and Celtic speaking people would also have been meaningful.

Someone at eurogenes had recently asked about how much modern South Asians are connected to Scythians rather than to earlier steppe groups. Maybe it could have been helpful here if the paper had also compared modern populations from different parts of India against the IA Scythian samples.

Maybe some future paper will revisit the Scythian aDNA samples and look into such questions.

How are you arriving at a linguistic conclusion based on a few plots? So now the very rich L23+ Yamnaya and Afanasievo isn't IE because of ..?

I do agree that the recent CWC data certainly draws a strong link between R1a-Z645 with CWC (Balto-Slavic) and a eastern cousin who founded Andronovo (Indo-Iranian) and came from the eastern peripheries of the European steppes.

That said, it doesn't explain any of the Centum families of language, and certainly Bell Beaker looks a little bit different. Which is predominantly LBK + Latvian_HG + Yamnaya. This interesting ethnic mix may have been further west than CWC despite being from a culture that superceded the bulk of west-central Europe and even some former CWC territory.

ak2014b: " I'm interested to know if modern Hungarians have a high relation to Scythians and Sarmatians too, as a connection to one or both has frequently been suggested."

Contemporary Hungarians fit very well to their Geographical position in comparisons, so I would be surprised if they had special genetic connection to Scythian. Also, if you looking outside the scientific community, there are a lot of connections "suggested", starting with the one that draws Hungarian ancestry from the Sirius, going toward less surreal but still very implausible ones like Sumerian or Japanese connections.

I have an open mind where PIE ultimately came from because we need more samples from Southern Europe,Anatolia,and India.But saying Yamnaya and CWC didn't speak IE seems crazy unless the Haak and Allentoft researchers were completely bonkers.

If Ukraine_N1 were the original IE than you have a clear path via this cline to BB (Italo-Celtic), Germanic have links to Balto-Slavic stronger than anyone here suppose, Greek and other Balkan languages - just google "Zyndram hill" (some Mycenaean-like Balkan network reached South Poland before Mycenaeans appeared in Greece).

And as they dwell at the Black Sea... Anatolia is just on the other side... but as you say, we need more DNA.

Indo-Iranian?

Nirjhar, what "yatsy tata, tatsy syn" means?

;-)

I'm just giving you a hypothesis. You're job is to prove that it is false. This is the fun of science.

We know for a fact from haplotypes that the ancestral slav possessed a genome similar to, or just 'south' of poles, not balts. You cannot just draw a cline from south slavs to balts, and then presume that all of them derived from some ancestral balto-slav expansion of a 'hyper-estonian' genome all the way out in HG-land into a Bell-Beaker like substrate in the rest of E Europe; the ellipse the populations make on PCA is very misleading, and in this case is produced by HG survival on one side and EEF introgression on the other.

This is ignoring the fact that Eastern Europe around Poland and the Baltic states was Corded ware-like post Bronze-age--in the case of Latvia even Yamnaya-like--not Bell-Beaker-like, so there is no Bell Beaker substrate to expand into. To see the genetic changes post bronze age, we should be drawing a line from Corded Ware to present-day balto-slavs, in which case we see that HG and Neolithic portions of ancestry have increased, more strongly in balts and slavs respectively, and the present day populations are more 'northwestern' then their bronze age predecessors, probably due to increased mixing with the local HG substrate, and then gene flow with the rest of Europe. After all, the balts were farmers when they emerged in history, which is not what a mix of HGs and pastoralist cultures, like those implied by the autosomes in the Siberian steppes post-Afanasievo, should lead us to expect.

You're probably right. Maybe only the Magyar conquering elite of the day carried a Sarmatian signal. I can only find this mention of Sarmatians in the Ethnic affiliations and genetic origins of Wikipedia's Hungarians page

Anthropologically, the type of Magyars of the conquest phase shows similarity to that of the Andronovo people,[78] in particular of the Sarmatian groups around the southern Urals.[79] The Turanid (South-Siberian) and the Uralid types from the Europo-Mongoloids were dominant among the conquering Hungarians.[80]

It also shows that the percentage of Asiatic presence in the modern Hungarian population's gene pool is low, though not (yet) non-existent, and higher than some other European nations. The Hunnic aDNA sample's L seems to have left no mark in the present either, going by the modern Hungarian Y haplogroups listed there.

Despite various invasions of Altaic peoples in Europe, no significant impact from such Asian descent is recorded throughout southern and central Europe.[116]

Is Turkey's population the only one so far west, of those with a recent history of Asiatic migration, that (still) has a more noticeable Asiatic ancestry? It's variously estimated at 13-15% and 21.7%, though I'm not sure why they're attributing the Asian input as possibly South Asian.

Was the migrant population to Turkey simply larger?

In all three cases, Hungary, Bulgaria and Turkey, I'd like some comparisons of aDNA starting from the immediate post-Asiatic migration period up to the present. It will be interesting to see if Asiatic signals were always about as low as now. Or whether they have only decreased over time, such as by dilution, since the Turkic Bulgars are described as merging with previous people and becoming Slavicised. Or whether in the past these Asiatic signals were largely exclusive to the elite migrant rulers.

The scythian paper is truly excellent. So we see that, other than haplotype sharing with Buryat, Altaian and Mongol (i.e. a S Siberian ancestral population) Turkics are also distinguished from other populations, including other Central Asians, by sharing of East Scythian segments, from the supp materials pg 13.

Quite interesting to trace the boundary between turkics and non-turkics and see this reflected in the segments exactly. Seems to imply that a wave of Western Scythians poured into C Asia, possibly overlaying a prior pulse of Andronovo-likes, reaching all the Iranic populations, followed by a wave from E Asia, together with the East Eurasian haplotypes characteristic of Turkics.

Interesting also that Okunevo, once again, shows its 'leapfrogging' affinities with Native Americans and Central Siberians (i.e. kets and Nganasan) to the exclusion of Beringians. At least, ADMIXTURE detects shared drift with Native Americans and Central Siberians in Okunevo but not with Beringians, when drift in these populations is tracked separately in different components at high K.

We have a relatively good grasp of the genetic turnovers in the N and E Steppes it seems. First a wave of Afanasievo-likes, then mixing with local Nganassan-like foragers with NAm affinities in Okunevo, then 50-50 mix of Afanasievo and Nganassan/Ket-likes in Karasuk. By the IA East Asian ancestry proper starts coming in; by the Turkic expansion almost as much East Asian ancestry as Ket-like ancestry was carried, together w the East Scythian Karasuk segments, by the Turks into Central Asia.

Also seems to provide circumstantial evidence for the idea that the Xiongnu had genetic and linguistic relations with Yeniseians such as Kets, since the East Asian substrate of the earliest East-Asian admixed inhabitants of the Eastern Steppes was Central-Siberian like.

Okunevo could indeed be partially ancestral to Nganasans but not to modern Beringians, in which case we're looking at a situation which is analoguous to ADMIXTURE showing South Asian or Native American in MA-1.

Nganasan ethnogenesis overall postdates Okunevo, it's likely quite recent (http://www.encyclopedia.com/places/commonwealth-independent-states-and-baltic-nations/cis-and-baltic-political-geography/nenets). For instance, at K=7/8 when Nganasan component hasn't formed, they have a significant southern shift compared to Beringians. This should be in line with the Broushaki et al. paper which models Nganasans as 10% Selkup 90% Dolgan. Okunevo has relatively much smaller southern component at that level, and its ratio of Beringian and Native American looks similar to Eskimo.

Could be something as simple as this: Okunevo's more "Native American" than Chukchis or Koryaks which maximize the Beringian component, so once the Nganasan drift is accounted for the excess goes into Native American. Nganasan + Beringian combo wouldn't be "Native" enough since Nganasans are Han-shifted compared to Beringians.

We might also speculate that MA-1 could be ancestral to something but is too low coverage or too temporally separated from moderns to show preferences. But indeed no certainty there.

This is ignoring the fact that Eastern Europe around Poland and the Baltic states was Corded ware-like post Bronze-age--in the case of Latvia even Yamnaya-like--not Bell-Beaker-like, so there is no Bell Beaker substrate to expand into.

Very good point!

http://www.archaeology.org/news/2556-140930-poland-bell-beaker

A 4,000-year-old ritual site has been unearthed on a hilltop in northeastern Poland. Fragments of decorated cups and bowls made by the Bell Beaker culture were found surrounded by burned bones and a fragment of an amber bead. A second amber object was found nearby. “Amber was an exotic and prestigious material for the Bell Beaker communities, and never before found in Podlasie.

Podlaskie voivodeship borders Lithuania and we already have Beaker sites found there.

Maybe Slavs are simply children of the Amber route?

Movement back and forth of both populations along the same route will produce the impression of Beaker substratum in Poland.

I wonder why do the eastern Scythians look like a straight mix of Yamnaya and East Asian. Where did the European_MN admixture present in the area go? And where did the Yamnaya-like people come from (the steppe was Srubnaya-Andronovo dominated in the previous phases, all with European admixture).

@Arza

the paper about that discovery that marks a new frontier for the Bell Beaker phenomenon (east Poland, border with Belarus) was uploaded to academia.edu the other day.

http://www.archaeology.org/news/2556-140930-poland-bell-beaker

I'm sure that someone here (whose initials are OM) will like some of the findings and conclusions ;)

We know for a fact from haplotypes that the ancestral slav possessed a genome similar to, or just 'south' of poles, not balts.

But you must also admit, that if we are looking at the trade route, and not a "regular" cline, than any haplotype from along this route could take over other populations. E.g. some chieftains that controlled specific points of the route could spread their sons to control even bigger part of this path.

My guess would be a warrior elite's long-term reproductive success is a balance between social status and casualty rate and the Ottoman pressure meant the Magyar elite's casualty rate was too high leading to replacement from below.

I'm not sure I understand correctly those figures 10 and 11. It seems that all the populations analysed are "forced" to choose between 4 "components" (?):

- Descended from Western Scythians- Ancestral relatedness to Western Scythian- Descended from Eastern Scythian- Ancestral relatedness to Eastern Scythian

So that populations that probably have nothing to do with Scythians (Yakuts, Han) turn out close to 100% 2Ancestral relatedness with Scythians", or Azeris turn out close to 100% "Descended from Scythians", just because what else could they choose?

@ Alberto: I wonder why do the eastern Scythians look like a straight mix of Yamnaya and East Asian. Where did the European_MN admixture present in the area go?

How certain are we about that? I only say because I don't have the knowledge of the precise samples - IRC from Laz 2016, there are only like 3 Steppe_MLBA from the same general area where Afanasievo was found, and then where the East Scyths turn up. There are also a few outliers in the ADMIXTURE which are minimally admixed with Europe_MN like components (one of these shows some minimal East Eurasian admixture).

Looking at the data table for sample origin from Laz 2016 (Supplement Table 1), the 3 Steppe_MLBA who are outliers for latitude are RISE500, RISE503, RISE505 and all from Andronovo culture (lat 85.447 like Afanasievo vs the others are 50-56). Does anyone know if these samples are outliers from other Andronovo when modelled with mixes of Europe_MN, Steppe_EMBA? In an ideal world where everything's simple they had very minimal European_MN who were mostly derived from Afanasievo culture absorbed by Andronovo culture expansions ;).

Or is it forced to choose between two components (represented by ancestral relatedness) while the "descended" implies actual ancestry? Looks like the latter given how little "descent" the far eastern populations have.

@Alberto ”I wonder why do the eastern Scythians look like a straight mix of Yamnaya and East Asian. Where did the European_MN admixture present in the area go? And where did the Yamnaya-like people come from (the steppe was Srubnaya-Andronovo dominated in the previous phases, all with European admixture).”

Maybe Srubnaya-Andronovo and early Sarmatians with EEF were Indo-Aryans and eastern Scythians simply do not descend from them. We know that Indo-Aryans were defeated by Turkics on the Central Asian steppe. In the French thesis, Altaian Sagsai culture (1400-900 BC) already looked very much Turkic with R1a - Z93 x 4, Q1a3 x 3, C - M130 x1 and lots of East Asian mtDNA. They did not necessarily have any EEF. At some point they started pushing westward.

The first Yamnaya Samara / Afanasievo like migrations (c. 3400) were surely not Indo Aryan. They were an admixture of WHG/EHG and CHG without EEF/Anatolia Neolithic. Maybe the origin of Tocharian is in these cultures. I could even be so revolutionary and propose that Eastern Yamnaya like cultures gave rise also to pre-Proto-Turkic.

Arza, your entire premise lies on the assumption that modern Slavs are a combination of two populations only. Of course far NE Euros are pulled in the direction of a no man's land compared to C Europe, having increased affinity to WHG and EEF in an odd 'Northwestern' combination such that no single source can account for it, but the whole point is there does not need to be a single source for it.

Furthermore we already know that CW in Latvia and CW in Germany are very similar, the ones in Germany just further East, and CW in Lithuania resembles straight Yamnaya. Unless you claim that CW in Poland resembles Czech BB, or later BB replaced CW 100% in the autosome in E Europe, or say the Ukraine_N plus BB combo was hiding in Saami-land, there is absolutely no way you your scenario will work.

The plots from the paper are extremely inacccurate, the CW genomes are plotting w Central Europeans when we know they are on accurate plots they are close to but still outside the range of modern genetic variation on the N Euro plain, so the Kud3 will most definitely not plot like RISE568.

Looking at their PCA; Narva+Kunda like Latvia_HG -> look like they work as mostly WHG (but look on PCA like they could be modelled 0.5 Loschbour+0.5SHG), PWC distinct (with what looks from PCA like as much HG ancestry as Steppe_Eneolithic, also previously shown), Baltic_BA samples have a distinct position (looks clinal between Yamnaya and PWC). MN_TRB looks like could have a slightly different position based on 3 samples (if the trend for their positon held true). 2x new EHG samples.

f3 heatmap shows structure in EuroHG: Rachot88, Rochedane and Loschbour have a particularly intense pattern of sharing among the WHG / Villabruna cluster. Rochedane also has a stronger relationship with Villabruna. La Brana has a slightly reduced relationship with the KO1, Kunda and Narva compared to the Loschbour, Ranchot, Rochedane. f3s also show slightly (but significantly?) stronger relationship between Lithuanian / Estonian with Narva / Kunda than with WHG.

But you must also admit, that if we are looking at the trade route, and not a "regular" cline, than any haplotype from along this route could take over other populations. E.g. some chieftains that controlled specific points of the route could spread their sons to control even bigger part of this path.

So the signature of shared haplotypes are from South Poles and only shared with Slavs, but the genetic expansion is from 'hyper-Estonians' from Baltic territory? I suppose the genes from the hyper Estonians spread without passing through chromosome segments, flying through the air maybe?

"The first Yamnaya Samara / Afanasievo like migrations (c. 3400) were surely not Indo Aryan. They were an admixture of WHG/EHG and CHG without EEF/Anatolia Neolithic."

If farmers encroaching onto the steppe to the limit of viability was the catalyst for PIE developing on the other side of the limit then in the earliest phases couldn't the new culture have spread over the steppe before they'd mixed much with the farmers?

(Arza, this coincides sample temporally with the timeframe of your BB abstract) Its very close to corded ware, and present-day poles indeed require ancestry from the 'NW' direction to get to their present position, not from 'BB+Ukraine_N' types.

@Grey - "If farmers encroaching onto the steppe to the limit of viability was the catalyst for PIE developing on the other side of the limit then in the earliest phases couldn't the new culture have spread over the steppe before they'd mixed much with the farmers?"

EEF stands for Early European Farmers. They had mixed with farmers - just not European ones. Hence where they got their CHG component from.

@David "If it is indeed based on ADMIXTURE, then they really need to back it up with some robust formal stats and qpAdm, because ADMIXTURE is not a formal mixture test."

I'm not sure why you are so skeptical of this, as if anything it adds further support to the Kurgan Hypothesis. Mixing between EHG and CHG had to happen before before the initial IE expansion if IE is to be a major source of CHG, or else only some IE groups would have had CHG.

I didn't even use the word "Satem" - You did. I simply stated the languages categorized as "Centum" don't fit into your little equation. You're the one bringing up the linguistic argument to paraphrase: "Yamnaya was not IE speaking". How can you arrive at this conclusion?

The data states CWC were R1a, and BB, including the Czech samples were R1b. Likewise, Andronovo was R1a, and Yamnaya was R1b. How much more basic do we need to get?

@ Ryukendo, I may not be following the conversation, check out the Baltic_BA population in the new paper - http://biorxiv.org/content/early/2017/03/03/113241. Very late Bronze Age samples (but well pre-Slavic expanion), at the beginning of Central European Iron Age with high HG ancestry. Seems distinct.

Re: PL_N17, I am not sure I try to model Poles as that + a single other population, as it would seem to imply PL_N17 mixing with PWC to get a sensible outcome (approx. 20% PWC 80%) if you took a single population, while PWC didn't exist so late. Or a complex mix of late survivors. Plus it is not so clear that PL_N17 is typical for the centroid of it's population - Central LNBA is highly heterogenous.

May make more sense to pick a Central_LNBA average (Beakers+Unetice) then combine with Baltic_BA.

I would agree with you that Slavic expansion likely not from a Baltic_BA like population though.

"EEF stands for Early European Farmers. They had mixed with farmers - just not European ones. Hence where they got their CHG component from."

right but same point - if a remote region of steppe expansion doesn't have a specific component that is found elsewhere couldn't it simply mean the earliest expansion happened before that particular mixture - and later expansions didn't get that far?

Arza's idea was that the Balto-slavs formed an ellipse/pyramid with Estonians at the tip pointing away from the mass of Europeans as a whole, so the Balto-slavs could be conceived of as a single population similar to a 50/50 mix of an atypical BB Czech plus Ukraine N, which occupies the right position, so the Balto-slavs expanded with a Ukraine_N+BB Czech like population deep into Eastern Europe, to create this pyramid/ellipse shape. But this was not the case, as that pattern was created by 'complex admixture' with sociocultural remnants after Corded Ware, like you said, followed by gene flow with the rest of Europe, so EEF and WHG rises and pulls the Balto-Slavs towards the 'Northwest', which is only problematic if we decide that a single 'northwestern' population was the reason for this. The paper here shows neatly that the ellipse he is talking about is not a sign of a movement, that the Balts on one hand were the result of local admixture with HGs and the Slavs were a separate phenomenon from a more EEF rich nucleus, and the whole bunch later got more EEF ancestry, more or less confirming the basic scenario.

and then picture the various potential match-upsthen it's possible to imagine a model where specifically wetlands HGs can hold their own at the edge of farming viability

#

maybe it's situations where an equilibrium of population density creates a static border that cultural and technological innovations can transfer without population displacement (e.g Wei river valley?)

AWood said... "@Arza, I didn't even use the word "Satem" - You did. I simply stated the languages categorized as "Centum" don't fit into your little equation. You're the one bringing up the linguistic argument to paraphrase: "Yamnaya was not IE speaking". How can you arrive at this conclusion? The data states CWC were R1a, and BB, including the Czech samples were R1b. Likewise, Andronovo was R1a, and Yamnaya was R1b. How much more basic do we need to get? Actually no... Bell Beaker, including Mr. Czech are pretty much modern North West Europeans".

Ahahahahahahahahahahahahahahahahahahahah

Yamnaya was R1b at the L23 level, which is also mine, in Italy from 6100 (or perhaps 7200 or 8100 years). About all the rest of the R1b1 haplotypes search in my 10000 letters, perhaps now many more...

Haak and company were careful to leave open the possibility that Yamnaya only brought a subset of IE to some areas of Europe.Maybe they were being too cautious.At any rate I keep harping about Anatolia and Greece because PIE origin depends on what those areas looked like during the Bronze Age.

Hmm Mittnik and Krause et al, i.e. the other, bigger paper mentioned by Matt, have Narva culture and Kunda culture virtually identical to WHG. This is interesting though, that CCC is close to EHG and Narva+Kunda are almost pure WHG, don't they geographically overlap? Whats the chronology again?

Wow interesting, thanks Rob (and Sam). So the picture seems to be that the population switches to EHG-shifted by the late Neol, but by that time the LBA Baltic genomes had mixed with the prior WHG Narva, making them somewhat Lithuanian-like already. Looking at the graph, Comb Ceramic arrives in Estonia first, and elsewhere later. The Jones et al Latvia MN sample (which happens to be CCC, apparently) also contains a slice of ENA, and improves the fit for Estonians and Finns but not Latvians and Lithuanians. David, I recall you saying that its possibly N1c. Am I right to say that some archaeologists think that Comb Ceramic marks the first arrival of Uralic languages to NE Europe? Just doing some pattern-matching...

@ Arza

Arza, at dimension 3 or 4 of some Europe PCA plots, there emerges a Iberian EEF vs Anatolian EEF dimension, and most of the scores make sense, e.g. Basque and Sardinian and Scottish, Orcadian and Icelandic on the Iberian end and Greek and Corded Ware and Yamnaya and Belarusian on the Anatolian end. But there is always one dot that doesn't behave properly: Andronovo. It always ends up in the Iberian end, and so it picks up Iberia EN in nMonte most of the time. In such cases you have to use your judgement. Of course we can propose giant movement of Iberian EEF to Eastern Europe to create Andronovo, but that is just one point which is subject to noise, and that behaviour is not found in Srubnaya, Sintashta, etc.

If there are parsimonious scenarios, e.g. pick up of increased WHG ancestry locally such that the 'Northern' pull is already sufficient in the LBA Baltic genomes, which we literally see occuring in Mittnik et al, then we should not propose very difficult or complicated situations, such as the idea that there is a Czech BB + Ukraine N mix for CCC. Why is Czech BB the only sample that is there? Where are the rest of the BBs? Why only Ukraine N + Czech BB attracted to drift in Balto Slavs in dimension 6? Etc.

I don't have any strong opinions at the moment about when N1c and Uralic languages arrived near the Baltic.

It seems to me that Latvia_MN2 does carry some post-ANE Siberian/Nganasan-related ancestry that is missing in EHG and EBA steppe groups. But Latvia_MN2 is a female, so my speculation that she belonged to N1c was misplaced.

I gather that CCC arrives in Estonia around 4000 BC, but is earlier further east, and that there is some overlap with Narva settlements (which could result in a later rise in WHG when they assimilated). Latvia_MN1 and MN2 lived in the overlap period, I think, and the former seems to be WHG/Narva while the latter (a woman) is EHG/CCC.

CCC as Uralic used to be popular but nowadays seems to be giving way to the view of Early Bronze Age and later waves from the Volga-Ural region. I don't think there's any general agreement on the question.

RKThe CCC in the Copenhagen paper was R1a, but xZ645, a nowadays rare lineage in Europe.

It all seems to suggest that N1c arrived to the Baltic very late- after 200 Bc, when considering all these samples collectively.

The other thing is that, yes, it seems Baltic CWC individuals continued to mix with local WHG Foragers LbA, as well as experiencing gradual "southern" admixture, pointing to Bronzes, Amber and a rise in LP. They single out an individual from Kivutkalns who plots with CE LNBA instead of Baltic LNBA

I see RISE568 as an outlier, a migrant. Just as a sign that in some other place similar population lived.

Of course we can treat this sample as an Andronovo sample you've mentioned. Let's say that we drop RISE568 from the spreadsheet. Is this problem solved? No, because you still have those Hyper Latvians. Are they outliers too? We should drop half of the Balto-Slavs one by one?

So maybe we should drop the whole PC6 dimension?But then is PC1 vs. PC7.PC2 vs. PC5 also looks similar.

My reasoning is that if WHG/EFF doesn't work for those Hyper Latvians, but there is another solution that additionally works for all Balto-Slavs, then why we should switch to partially working solution in the half of this definitely-not-a-cline?

And when you'll apply this to all Balto-Slavs you'll realize that this is a cline. Pointing to Beakers. Crazy. But then you'll realize that RISE568 was found among those Beakers to which this cline is pointing. Even crazier.

Additionally this not-a-cline correlates with present geographical distribution - it goes from Czechs, through Western-looking Polish samples, Eastern Poles and Belarusians, Lithuanians and Estonians and it ends on Latvians.

More or less it looks like this:https://4.bp.blogspot.com/-L0Y3oyCvP10/WJS5NWk7OMI/AAAAAAAAAGU/iCLvbEXg9cwtTokT21i-i-9ansq2ve9MQCLcB/s1600/clinemap.jpg

You can see there some additional arrows. Today I didn't mentioned yet that the Finns, Vepsians, Karelians etc. are apparently joining this PC6 party. They stick to this not-a-cline all the time and basically they look like 3/4 Estonians/Lithuanians and 1/4 Saami (+some Karelian_HG flavours). Something like this: